Jim and Artie arrive at the town of Willow Springs, only to find the once-thriving town seemingly empty. They go into the saloon and find everyone completely immobile but still alive. All of the money is missing and the bank safe has been blown open.
Jim meets with Governor Hawthorne, and admits they haven?t found anything yet and only one man died, of unknown causes. Artie is working on analyzing the mysterious paralysis. Hawthorne tells Jim that he was ?condemned? to his current position and plans to return to Washington in triumph. Hawthorne shows Jim a letter from Grant offering him assistance and he plans to make Jim and Artie the scapegoats if there?s no solution pending. A clerk brings in a distress message from Sands Hill and Jim quickly takes off to investigate.
Artie arrives at the morgue and meets with Dr. Kirby, who has volunteered to analyze the body. Kirby shows that the nerves have been attacked by some toxic substance, but then begins to suffer paralysis himself. He directs Artie to a bag containing an injection but someone knocks the agent out from behind before he can get it.
Robbers are pillaging the town of Sand hills as the paralyzed townfolk stand in the streets. Their leader, Coley Rodman, orders the men to leave with their plunder, unaware that Jim has been pretending to be paralyzed. Once they leave, Jim follows them to an abandoned fort and climbs over the wall that night. He drugs a guard unconscious and sneaks into the compound, while Coley counts the money and realizes someone took more then their cut. He confronts one of the men, Frank, and the other grab him and search his wallet. Coley beats up Frank and then guns him down, knocking Frank into a support post. It shatters, weakening the ceiling so that Jim falls down into the room. Jim fights the men, knocks out the lights, and makes a run for it, using a wagon as a diversion. He takes refuge in a room and finds himself confronting a Chinese woman, Anna. She agrees to hide Jim in a room filled with lab animals.
Coley and his men haven?t found Jim and discuss leaving their patron, ?the Doc.? Anna explains that her father studied with Lister then went to China and met her mother. He failed to cure the Emperor?s wife so the Emperor had Anna?s mother killed and destroyed her father?s reputation. She says her father is the gang?s prisoner and doesn?t know what they?re doing, and the gang is distributing the plague through the towns? water supplies. Their next target is San Francisco, so Jim leaves to warn the city. Jim climbs over the fort wall and runs into the desert. The men catch up to another figure and grab him, only to find it?s Artie.
Jim gets to Hawthorne and recommends several precautionary methods. Hawthorne is skeptical and reveals the doctor vanished and Artie had a concussion then went to search for Jim. Jim takes over shaving the governor?s throat and Hawthorne is more willing to agree with Jim. Jim goes back to the fort to get the girl, her father, and Artie.
Artie is strapped to a table and Coley prepares to interrogate him with some hungry ferrets. Artie finally ?confesses? that he?s a crook looking for a place to hang out but Coley doesn?t believe him. Anna intervenes without luck but then the doctor arrives? Dr. Kirby, who is no prisoner but rather in charge of the whole operation.
Jim sneaks back into the fort using pitons and is forced to pull a guard over the wall where he screams. Coley hears the scream and goes to investigate. Kirby is displaying his research to Artie, thankful for someone smart enough to appreciate his work. Jim comes busting in and a furious Kirby breaks up the resulting fight and Jim realizes he?s disguised. Anna comes in and her father realizes she knows Jim. Anna confesses that she helped Jim earlier and her father is upset at her betrayal. He prepares an injection of his newest lethal culture and orders her to inject the agents. She does so and gang takes the paralyzed men into the storage room. Once Coley and his men leave, Jim and Artie snap out of it: Anna faked the injections.
Coley and Kirby argue over their differing goals, but Kirby is insistent they use his bacillus on San Francisco, killing everyone. In the storage room, Jim traces an outline of Artie on the door with chalk then uses a chemical pellet from his belt to make a thermite solution so they can burn through the door. Coley sends one of his men to dispose of them and Jim kicks the man off the stairway. Jim goes to confront Kirby who can?t understand how Jim survived his ?perfect? germs. Jim tries to convince the clearly deranged Kirby to surrender without much luck. Coley busts in and Jim attacks him and his men. Kirby tries to get them to stop and goes for his gun, and Coley guns him down. Jim knocks the other man into Coley and then disarms and captures him. Jim sets the lab on fire, destroying Kirby?s work.
Later on the Wanderer, Jim assures Anna there?s no chance of an epidemic They plan to show her a good time in San Francisco until she mentions her fianc? who will meet them, and they can all be good friends. They have a four-way toast including the missing fianc?e.